Conformational entropy in molecular recognition by proteins

Molecular recognition by proteins is fundamental to almost every biological process, particularly the protein associations underlying cellular signal transduction. Understanding the basis for protein-protein interactions requires the full characterization of the thermodynamics of their association. Historically it has been virtually impossible to experimentally estimate changes in protein conformational entropy, a potentially important component of the free energy of protein association. However, nuclear magnetic resonance spectroscopy has emerged as a powerful tool for characterizing the dynamics of proteins. Here we employ changes in conformational dynamics as a proxy for corresponding changes in conformational entropy. We find that the change in internal dynamics of the protein calmodulin varies significantly on binding a variety of target domains. Surprisingly, the apparent change in the corresponding conformational entropy is linearly related to the change in the overall binding entropy. This indicates that changes in protein conformational entropy can contribute significantly to the free energy of protein-ligand association.     

Inactivation and Conformational Changes of Lactate Dehydrogenase M4 during Unfolding in Urea Solutions

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Protein activity regulation by conformational entropy

How the interplay between protein structure and internal dynamics regulates protein function is poorly understood. Often, ligand binding, post-translational modifications and mutations modify protein activity in a manner that is not possible to rationalize solely on the basis of structural data. It is likely that changes in the internal motions of proteins have a major role in regulating protein activity, but the nature of their contributions remains elusive, especially in quantitative terms. Here we show that changes in conformational entropy can determine whether protein-ligand interactions will occur, even among protein complexes with identical binding interfaces. We have used NMR spectroscopy to determine the changes in structure and internal dynamics that are elicited by the binding of DNA to several variants of the catabolite activator protein (CAP) that differentially populate the inactive and active DNA-binding domain states. We found that the CAP variants have markedly different affinities for DNA, despite the CAP?DNA-binding interfaces being essentially identical in the various complexes. Combined with thermodynamic data, the results show that conformational entropy changes can inhibit the binding of CAP variants that are structurally poised for optimal DNA binding or can stimulate the binding activity of CAP variants that only transiently populate the DNA-binding-domain active state. Collectively, the data show how changes in fast internal dynamics (conformational entropy) and slow internal dynamics (energetically excited conformational states) can regulate binding activity in a way that cannot be predicted on the basis of the protein's ground-state structure.     

大熊猫肌酸激酶热变性中活性与构象变化的比较

比较了大熊猫肌酸激酶在各种不同温度下热变性时，活性变化与构象变化的速度常数。结果表明在较低温度下，酶的失活速度与构象变化速度相当．而在较高温度下变性时酶的失活速度快于构象变化速度。这表明酶分子的活性部位的微区构象比整个分子的构象具有更大的易变性或柔性。     

人血清白蛋白与吩噻嗪相互作用时的构象变化研究

研究了人血清白蛋白与药物吩噻嗪相互作用时的荧光淬灭及构象变化情况．结果表明：吩噻嗪通过静态方式对HSA的荧光进行淬灭,并与HSA形成了复合物;吩噻嗪在与人血清白蛋白相互作用时未引起该蛋白质构象的变化．因此,吩噻嗪作为药物在用于某些疾病的治疗时,不会影响到人血清白蛋白这样的传输蛋白的正常生理功能．本研究对药理学和临床医学具有重要意义．     

杂色鲍碱性磷酸酶在DMSO溶液中的活力与构象变化的研究

以二甲亚砜（DMSO）为效应物．研究其对杂色鲍碱性磷酸酶（ALP）活力的影响，结果表明：该酶的剩余活力随着DMSO浓度增大而迅速下降，当DMSO浓度达40％，酶活力几乎完全丧失．说明DMSO对杂色鲍ALP有明显的失活作用．导致酶活力丧失50％的DMSO浓度为17％．在较低DMSO浓度（〈20％）的失活是可逆的反应过程．动力学研究表明，该酶的失活过程属于混合型．进一步测定游离酶（E）和酶底物络合物（ES）与DMSO的结合常数（K1和K1s），结果表明K1〈K1s即说明底物存在对酶被DMSO的失活作用有一定的保护作用．应用荧光发射光谱研究杂色鲍ALP经DMSO微扰后的分子构象变化情况，随着DMSO浓度增大，荧光强度逐渐增强．但发射峰未发生明显变化现象．说明酶分子中的生色基团残基的微环境发生了一定的变化．     

SDS滴定时氨基酰化酶的溶液构象和活力变化的研究

本文以荧光发射光谱和紫外差吸收光谱的方法，研究了ＳＤＳ滴定氨基酰化酶溶液时构象变化的情况，同时测定了相应的物的活力的变化。实验结果发现酶的构象变化程度与相应的失活的程度大致平行。这表明酶基酰化酶构象的完整性是酶具有催化活力的基础。     

Electrically driven directional motion of a four-wheeled molecule on a metal surface

Propelling single molecules in a controlled manner along an unmodified surface remains extremely challenging because it requires molecules that can use light, chemical or electrical energy to modulate their interaction with the surface in a way that generates motion. Nature's motor proteins have mastered the art of converting conformational changes into directed motion, and have inspired the design of artificial systems such as DNA walkers and light- and redox-driven molecular motors. But although controlled movement of single molecules along a surface has been reported, the molecules in these examples act as passive elements that either diffuse along a preferential direction with equal probability for forward and backward movement or are dragged by an STM tip. Here we present a molecule with four functional units--our previously reported rotary motors--that undergo continuous and defined conformational changes upon sequential electronic and vibrational excitation. Scanning tunnelling microscopy confirms that activation of the conformational changes of the rotors through inelastic electron tunnelling propels the molecule unidirectionally across a Cu(111) surface. The system can be adapted to follow either linear or random surface trajectories or to remain stationary, by tuning the chirality of the individual motor units. Our design provides a starting point for the exploration of more sophisticated molecular mechanical systems with directionally controlled motion.     

Conformational changes associated with ion permeation in L-type calcium channels

The mechanism by which ions deliver their message to effector proteins involves a change in the protein conformation which is induced by the specific interaction of the ion with its binding site on the protein. In the case of an ion-channel protein, conformational changes induced by permeant ions and the consequences for channel function have received little attention. Here we report that binding of permeant cations to an intra-channel binding site of the dihydropyridine (DHP)-sensitive (L-type) Ca2+ channel leads to a conformational change which destabilizes the protonated state of a group on the external channel surface, and can shift its apparent pK value by more than 2 pH units. The lifetime of the protonated state correlates with the occupancy of an intra-channel binding site by the permeant cation. The demonstration of such conformational changes in a channel protein induced by the permeant ion has important implications for realistic models of the mechanism of ion permeation.     

Effect of Urea on Activity and Conformation of a Glycoprotein

Introduction In some enzymes, inactivation occurs before noticeable conformational change can be detected during denaturation by guanidinium chloride or urea[1-6]. Tsou[7] suggested that enzyme active sites are formed by relatively weak molecular interact…     

乙醇对鲍鱼碱性磷酸酶活力与构象的影响

以乙醇为效应物研究对鲍鱼碱性磷酸酶(ALP)活力影响的结果表明．酶的剩余活力随着乙醇浓度增大而迅速下降，乙醇浓度40％可使酶活力完全丧失．说明乙醇对鲍鱼ALP有明显的失活作用，JG50为13％．含较低浓度乙醇(30％)的失活过程是可逆的反应．测定乙醇对酶的失活作用机理．结果表明乙醇对鲍鱼ALP的失活作用是非竞争性机制，说明底物存在不影响乙醇对酶的失活作用．应用荧光光谱、紫外吸收光谱研究鲍鱼ALP经乙醇微扰后的分子构象变化，发现乙醇对酶分子构象有显的影响，酶的内源荧光强度随乙醇浓度增大而增强．荧光发射峰逐渐发生红移．紫外吸收光谱在276nm吸收峰随乙醇浓度增大而增强．这些结果表明．酶蛋白分子中的生色基团残基的微环境发生变化．     

The ABC protein turned chloride channel whose failure causes cystic fibrosis

CFTR chloride channels are encoded by the gene mutated in patients with cystic fibrosis. These channels belong to the superfamily of ABC transporter ATPases. ATP-driven conformational changes, which in other ABC proteins fuel uphill substrate transport across cellular membranes, in CFTR open and close a gate to allow transmembrane flow of anions down their electrochemical gradient. New structural and biochemical information from prokaryotic ABC proteins and functional information from CFTR channels has led to a unifying mechanism explaining those ATP-driven conformational changes.     

Control of conformational and interpolymer effects in conjugated polymers.

The role of conjugated polymers in emerging electronic, sensor and display technologies is rapidly expanding. In spite of extensive investigations, the intrinsic spectroscopic properties of conjugated polymers in precise conformational and spatial arrangements have remained elusive. The difficulties of obtaining such information are endemic to polymers, which often resist assembly into single crystals or organized structures owing to entropic and polydispersity considerations. Here we show that the conformation of individual polymers and interpolymer interactions in conjugated polymers can be controlled through the use of designed surfactant poly(p-phenylene-ethynylene) Langmuir films. We show that by mechanically inducing reversible conformational changes of these Langmuir monolayers, we can obtain the precise interrelationship of the intrinsic optical properties of a conjugated polymer and a single chain's conformation and/or interpolymer interactions. This method for controlling the structure of conjugated polymers and establishing their intrinsic spectroscopic properties should permit a more comprehensive understanding of fluorescent conjugated materials.     

姜黄素类化合物对体外非酶糖基化的抑制作用

比较研究了姜黄素、去甲氧基姜黄素、双去甲氧基姜黄素和姜黄素衍生物a对蛋白质非酶糖基化反应的终末产物(AGEs)的抑制作用,同时测定了它们与牛血清白蛋白的结合作用及其对牛血清白蛋白二级结构的影响.结果表明,4种姜黄素类化合物均有抑制作用,抑制效果依次为姜黄素,双去甲氧基姜黄素,去甲氧基姜黄素和姜黄素衍生物a;姜黄素类化合物与牛血清白蛋白有较强的结合作用并能引起蛋白质结构的变化.     

白术多糖的溶液构象及其变化

采用刚果红实验判断白术多糖WAM在溶液中的构象特征,通过测定不同溶液体系中多糖分子的黏度、比旋度、紫外吸收光谱和圆二色谱的变化来研究多糖构象及其变化规律.实验结果表明:WAM不具有螺旋结构,温度、金属离子、变性剂均可以使WAM构象发生改变.WAM在溶液中以无规则线团形式存在.     

尿素诱导的蛋白质变性现象的研究

通过对典型蛋白质变性实验结果的分析，发现在蛋白质变性研究领域中普遍使用的二态模型所描述的过程，与真实蛋白质变性过程并不相符．在分析已有的实验结果的基础上，给出了反映蛋白质变性过程特征的新表示形式．这一形式表明蛋白质分子变性是一个构象渐变的过程，同时强调在一定浓度的尿素溶液中蛋白质分子均处于相同的构象态．从尿素分子与蛋白质肽链上的相邻二肽形成双氢键的假设出发，利用吸附反应动力学方法，得到了描述蛋白质变性特征的物理量与尿素浓度关系的表示式．结果表明理论值与实验值符合较好，说明建立的模型可较好地描述尿素导致的蛋白质变性现象．     

用红外光谱法研究聚氯乙烯的增塑机理

傅立叶变换红外光谱法用于探测增塑聚氯乙烯 (PVC)的构象和结晶的变化。研究中采用的增塑剂为邻苯二甲酸二辛酯 (DOP)、邻苯二甲酸二正丁酯 (DBP)和癸二酸二辛酯 (DOS)。用差谱技术在除去增塑剂对总的红外光谱的贡献后,研究在600～700cm^-1范围内由PVC增塑作用引起的构象变化。将增塑的PVC与未增塑的PVC光谱进行比较,结果发现增塑PVC的光谱中某些C—Cl伸缩振动光谱带有明显的位移,这个结论突出了增塑PVC的构象变化,这种变化取决于增塑剂的用量和种类。通过1426cm^-1 (TTTT构象、结晶 )和1434cm^-1 (无定形)吸收带的吸收度比值 ,研究了由PVC增塑作用引起的结晶变化,比值的大小与增塑剂的用量和增塑PVC的存放时间有关。根据构象和结晶度的变化可以确定增塑剂的增塑效果,为选择增塑剂提供了理论依据。     

Effect of calcium ions on the secondary structures of photosystemⅡ and its relations with photoinhibition

Calcium ions play an important role in the oxygen_evolving process of photosystem Ⅱ as demonstrated in many experiments. The changes of the secondary structures of PS Ⅱ induced by the depletion of Ca 2+ were reported. The results indicated that the removal of Ca 2+ led to the transition of α helix to turns and sheet structures. While Ca 2+ was re_added to the media, only the structures changed to turns could be recovered. The protein conformational changes of PS Ⅱ during the donor side photoinhibition induced by the depletion of Ca 2+ were also studied. This showed that the protein conformational changes differed between the control and Ca 2+ _depleted samples in a short period of illumination (within 10 min). However, the changes became similar when the illumination time was increased.     

Atmospheric CO2 forces abrupt vegetation shifts locally, but not globally

It is possible that anthropogenic climate change will drive the Earth system into a qualitatively different state. Although different types of uncertainty limit our capacity to assess this risk, Earth system scientists are particularly concerned about tipping elements, large-scale components of the Earth system that can be switched into qualitatively different states by small perturbations. Despite growing evidence that tipping elements exist in the climate system, whether large-scale vegetation systems can tip into alternative states is poorly understood. Here we show that tropical grassland, savanna and forest ecosystems, areas large enough to have powerful impacts on the Earth system, are likely to shift to alternative states. Specifically, we show that increasing atmospheric CO2 concentration will force transitions to vegetation states characterized by higher biomass and/or woody-plant dominance. The timing of these critical transitions varies as a result of between-site variance in the rate of temperature increase, as well as a dependence on stochastic variation in fire severity and rainfall. We further show that the locations of bistable vegetation zones (zones where alternative vegetation states can exist) will shift as climate changes. We conclude that even though large-scale directional regime shifts in terrestrial ecosystems are likely, asynchrony in the timing of these shifts may serve to dampen, but not nullify, the shock that these changes may represent to the Earth system.     

Mechanical twisting of a guest by a photoresponsive host

Molecular analogues of a variety of mechanical devices such as shuttles, brakes, unidirectional rotors and tweezers have been created. But these 'molecular machines' have not yet been used to mechanically manipulate a second molecule in a controlled and reversible manner. Here we show that light-induced scissor-like conformational changes of one molecule can give rise to mechanical twisting of a non-covalently bound guest molecule. To realize this coupling of molecular motions, we use a previously designed system: a ferrocene moiety with an azobenzene strap, each end of which is attached to one of the two cyclopentadienyl rings of the ferrocene unit, acts as a pivot so that photoisomerization of the strap rotates the ferrocene rings relative to each other and thereby also changes the relative position of two 'pedal' moieties attached to the ferrocene rings. We translate this effect into intermolecular coupling of motion by endowing the pedals with binding sites, which allow the host system to form a stable complex with a bidentate rotor molecule. Using circular dichroism spectroscopy, we show that the photoinduced conformational changes of the host are indeed transmitted and induce mechanical twisting of the rotor molecule. This design concept, which significantly extends the successful coupling of motion beyond the intramolecular level seen in synthetic allosteric receptors, might allow for the remote control of molecular events in larger interlocked molecular systems.